Description

Quality control of riboseq bam data

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing riboseq sample information
e.g. `[ id:‘sample1’, single_end

]

bam_ribo (file)

Sorted riboseq BAM file(s)

*.{bam}

bai_ribo (file)

Index for sorted riboseq bam file(s)

*.{bai}

meta2 (map)

Groovy Map containing TI-Seq sample information
e.g. [ id:'sample1', single_end:false ]

bam_ti (file)

Sorted TI-Seq BAM file(s)

*.{bam}

bai_ti (file)

Index for sorted TI-Seq BAM file(s)

*.{bai}

meta3 (map)

Groovy Map containing reference information
e.g. [ id:'Ensembl human v.111' ]

fasta (file)

Fasta-format sequence file for reference sequences used in the bam file

*.gtf

gtf (file)

GTF-format annotation file for reference sequences used in the bam file

*.gtf

meta4 (map)

Groovy Map containing information on candidate ORFs

candidate_orfs (file)

3-column (transIDstarttstop) candidate ORFs file

*.txt

meta5 (map)

Groovy Map containing information on riboseq P-site offfset parameter
files

para_ribo (file)

Input P-site offset parameter files for riboseq bam files

*.py

meta6 (map)

Groovy Map containing information on TI-seq P-site offfset parameter
files

para_ribo (file)

Input P-site offset parameter files for TI-seq bam files

*.py

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]

predictions (file)

txt file all possible ORF results that fit the thresholds

*.{txt}

all (file)

txt file similar to the predictions but do not use FDR (q-value) cutoff

*.{txt}

transprofile (file)

Output RPF P-site profile for each transcript. The profile data is in
python dict format, recording non-zero read counts at different
positions on transcript.

*.{py}

versions (file)

File containing software versions

versions.yml

Tools

ribotish
GPL v3

Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data.